library(ggplot2)
library(tidyr)
library(dplyr)
##
## Attaching package: 'dplyr'
## The following objects are masked from 'package:stats':
##
## filter, lag
## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union
library(scales)
### Read meta data
parvimeta<-read.delim("../data/CUteocintles/output/parvi33929_meta.tsv")
parviPlinksamples<-read.table("../data/genetic/output/T4465_33929_parvi.fam")
parvi_CV<-read.delim("../data/genetic/output/admixture/parvi/parvi_CV.txt", sep=" ")
## Plot CV
p <- ggplot(parvi_CV, aes(x=K, y=CV)) + geom_point(size=1) + geom_line()
p + theme(axis.title.x = element_text(face="bold", size=20),
axis.text.x = element_text(angle=90, vjust=0.5, size=16),
axis.title.y = element_text(face="bold", size=20),
axis.text.y = element_text(size=16))
### Get Q data and plot
for(K in c(1:42)){
## get data
Qval<-read.table(paste0("../data/genetic/output/admixture/parvi/T4465_33929_parvi.", K, ".Q"))
names(Qval)<-paste0("K", 1:ncol(Qval))
## Tidy data for ggplot
# get metadata of plink samples and add to Qtable
parvimeta<-parvimeta[parvimeta$INDIV %in% parviPlinksamples$V2, ]
Qval<-cbind(parvimeta$INDIV, parvimeta$LONGITUDE, parvimeta$LATITUDE, Qval)
names(Qval)[1:3]<-c("INDIV", "LONGITUDE", "LATITUDE")
# write file
write.table(Qval, file=paste0("../data/genetic/output/admixture/parvi/Qparvi_K", K, ".tsv"), sep="\t", quote = FALSE, row.names = FALSE)
# transfor to long format
Qval_long<-gather(Qval, key=Kgroup, value=Qadmixture, 4:ncol(Qval))
## Plot
# standar
plt<-ggplot(Qval_long, aes(x=INDIV, y=Qadmixture, fill=Kgroup)) + geom_col() +
theme(axis.text.x= element_blank())
# get color names in case it is needed match with other plots outside r
print("colors used")
print(scales::hue_pal()(K))
print(plt)
}
## [1] "colors used"
## [1] "#F8766D"
## [1] "colors used"
## [1] "#F8766D" "#00BFC4"
## [1] "colors used"
## [1] "#F8766D" "#00BA38" "#619CFF"
## [1] "colors used"
## [1] "#F8766D" "#7CAE00" "#00BFC4" "#C77CFF"
## [1] "colors used"
## [1] "#F8766D" "#A3A500" "#00BF7D" "#00B0F6" "#E76BF3"
## [1] "colors used"
## [1] "#F8766D" "#B79F00" "#00BA38" "#00BFC4" "#619CFF" "#F564E3"
## [1] "colors used"
## [1] "#F8766D" "#C49A00" "#53B400" "#00C094" "#00B6EB" "#A58AFF" "#FB61D7"
## [1] "colors used"
## [1] "#F8766D" "#CD9600" "#7CAE00" "#00BE67" "#00BFC4" "#00A9FF" "#C77CFF"
## [8] "#FF61CC"
## [1] "colors used"
## [1] "#F8766D" "#D39200" "#93AA00" "#00BA38" "#00C19F" "#00B9E3" "#619CFF"
## [8] "#DB72FB" "#FF61C3"
## [1] "colors used"
## [1] "#F8766D" "#D89000" "#A3A500" "#39B600" "#00BF7D" "#00BFC4" "#00B0F6"
## [8] "#9590FF" "#E76BF3" "#FF62BC"
## [1] "colors used"
## [1] "#F8766D" "#DB8E00" "#AEA200" "#64B200" "#00BD5C" "#00C1A7" "#00BADE"
## [8] "#00A6FF" "#B385FF" "#EF67EB" "#FF63B6"
## [1] "colors used"
## [1] "#F8766D" "#DE8C00" "#B79F00" "#7CAE00" "#00BA38" "#00C08B" "#00BFC4"
## [8] "#00B4F0" "#619CFF" "#C77CFF" "#F564E3" "#FF64B0"
## [1] "colors used"
## [1] "#F8766D" "#E18A00" "#BE9C00" "#8CAB00" "#24B700" "#00BE70" "#00C1AB"
## [8] "#00BBDA" "#00ACFC" "#8B93FF" "#D575FE" "#F962DD" "#FF65AC"
## [1] "colors used"
## [1] "#F8766D" "#E38900" "#C49A00" "#99A800" "#53B400" "#00BC56" "#00C094"
## [8] "#00BFC4" "#00B6EB" "#06A4FF" "#A58AFF" "#DF70F8" "#FB61D7" "#FF66A8"
## [1] "colors used"
## [1] "#F8766D" "#E58700" "#C99800" "#A3A500" "#6BB100" "#00BA38" "#00BF7D"
## [8] "#00C0AF" "#00BCD8" "#00B0F6" "#619CFF" "#B983FF" "#E76BF3" "#FD61D1"
## [15] "#FF67A4"
## [1] "colors used"
## [1] "#F8766D" "#E68613" "#CD9600" "#ABA300" "#7CAE00" "#0CB702" "#00BE67"
## [8] "#00C19A" "#00BFC4" "#00B8E7" "#00A9FF" "#8494FF" "#C77CFF" "#ED68ED"
## [15] "#FF61CC" "#FF68A1"
## [1] "colors used"
## [1] "#F8766D" "#E7851E" "#D09400" "#B2A100" "#89AC00" "#45B500" "#00BC51"
## [8] "#00C087" "#00C0B2" "#00BCD6" "#00B3F2" "#29A3FF" "#9C8DFF" "#D277FF"
## [15] "#F166E8" "#FF61C7" "#FF689E"
## [1] "colors used"
## [1] "#F8766D" "#E88526" "#D39200" "#B79F00" "#93AA00" "#5EB300" "#00BA38"
## [8] "#00BF74" "#00C19F" "#00BFC4" "#00B9E3" "#00ADFA" "#619CFF" "#AE87FF"
## [15] "#DB72FB" "#F564E3" "#FF61C3" "#FF699C"
## [1] "colors used"
## [1] "#F8766D" "#E9842C" "#D69100" "#BC9D00" "#9CA700" "#6FB000" "#00B813"
## [8] "#00BD61" "#00C08E" "#00C0B4" "#00BDD4" "#00B5EE" "#00A7FF" "#7F96FF"
## [15] "#BC81FF" "#E26EF7" "#F863DF" "#FF62BF" "#FF6A9A"
## [1] "colors used"
## [1] "#F8766D" "#EA8331" "#D89000" "#C09B00" "#A3A500" "#7CAE00" "#39B600"
## [8] "#00BB4E" "#00BF7D" "#00C1A3" "#00BFC4" "#00BAE0" "#00B0F6" "#35A2FF"
## [15] "#9590FF" "#C77CFF" "#E76BF3" "#FA62DB" "#FF62BC" "#FF6A98"
## [1] "colors used"
## [1] "#F8766D" "#EB8335" "#DA8F00" "#C49A00" "#A9A400" "#86AC00" "#53B400"
## [8] "#00BA38" "#00BE6D" "#00C094" "#00C0B5" "#00BDD2" "#00B6EB" "#00ABFD"
## [15] "#619CFF" "#A58AFF" "#D078FF" "#EC69EF" "#FB61D7" "#FF63B9" "#FF6B96"
## [1] "colors used"
## [1] "#F8766D" "#EC8239" "#DB8E00" "#C79800" "#AEA200" "#8FAA00" "#64B200"
## [8] "#00B81B" "#00BD5C" "#00C085" "#00C1A7" "#00BFC4" "#00BADE" "#00B2F3"
## [15] "#00A6FF" "#7C96FF" "#B385FF" "#D874FD" "#EF67EB" "#FD61D3" "#FF63B6"
## [22] "#FF6B94"
## [1] "colors used"
## [1] "#F8766D" "#EC823C" "#DD8D00" "#CA9700" "#B3A000" "#97A900" "#71B000"
## [8] "#2FB600" "#00BB4B" "#00BF76" "#00C098" "#00C0B7" "#00BDD1" "#00B7E8"
## [15] "#00AEFA" "#3DA1FF" "#8F91FF" "#BE80FF" "#DE71F9" "#F265E7" "#FE61CF"
## [22] "#FF64B3" "#FF6C92"
## [1] "colors used"
## [1] "#F8766D" "#ED813E" "#DE8C00" "#CD9600" "#B79F00" "#9DA700" "#7CAE00"
## [8] "#49B500" "#00BA38" "#00BE67" "#00C08B" "#00C1A9" "#00BFC4" "#00BBDC"
## [15] "#00B4F0" "#00A9FF" "#619CFF" "#9F8CFF" "#C77CFF" "#E36EF6" "#F564E3"
## [22] "#FF61CC" "#FF64B0" "#FF6C91"
## [1] "colors used"
## [1] "#F8766D" "#ED8141" "#E08B00" "#CF9400" "#BB9D00" "#A3A500" "#85AD00"
## [8] "#5BB300" "#00B81F" "#00BC59" "#00BF7D" "#00C19C" "#00C0B8" "#00BDD0"
## [15] "#00B8E5" "#00B0F6" "#00A5FF" "#7997FF" "#AC88FF" "#CF78FF" "#E76BF3"
## [22] "#F763E0" "#FF61C9" "#FF65AE" "#FF6C90"
## [1] "colors used"
## [1] "#F8766D" "#EE8043" "#E18A00" "#D19300" "#BE9C00" "#A8A400" "#8CAB00"
## [8] "#68B100" "#24B700" "#00BB49" "#00BE70" "#00C090" "#00C1AB" "#00BFC4"
## [15] "#00BBDA" "#00B5ED" "#00ACFC" "#42A0FF" "#8B93FF" "#B684FF" "#D575FE"
## [22] "#EB69F0" "#F962DD" "#FF61C6" "#FF65AC" "#FF6D8E"
## [1] "colors used"
## [1] "#F8766D" "#EE8045" "#E28900" "#D39200" "#C19B00" "#ACA300" "#93AA00"
## [8] "#73B000" "#41B500" "#00BA38" "#00BD63" "#00C083" "#00C19F" "#00C0B9"
## [15] "#00BECF" "#00B9E3" "#00B2F4" "#00A8FF" "#619CFF" "#998EFF" "#BF80FF"
## [22] "#DB72FB" "#EE67EC" "#FA62DA" "#FF61C3" "#FF66AA" "#FE6D8D"
## [1] "colors used"
## [1] "#F8766D" "#EF7F46" "#E38900" "#D59100" "#C49A00" "#B0A100" "#99A800"
## [8] "#7CAE00" "#53B400" "#00B823" "#00BC56" "#00BF77" "#00C094" "#00C1AD"
## [15] "#00BFC4" "#00BCD9" "#00B6EB" "#00AEF9" "#06A4FF" "#7698FF" "#A58AFF"
## [22] "#C77CFF" "#DF70F8" "#F166E9" "#FB61D7" "#FF62C1" "#FF66A8" "#FE6D8C"
## [1] "colors used"
## [1] "#F8766D" "#EF7F48" "#E48800" "#D69100" "#C69900" "#B4A000" "#9EA700"
## [8] "#83AD00" "#60B200" "#19B700" "#00BB48" "#00BE6B" "#00C088" "#00C1A2"
## [15] "#00C0BA" "#00BECF" "#00B9E1" "#00B3F1" "#00ABFD" "#46A0FF" "#8794FF"
## [22] "#B086FF" "#CE79FF" "#E46DF6" "#F365E6" "#FC61D4" "#FF62BE" "#FF67A6"
## [29] "#FE6E8B"
## [1] "colors used"
## [1] "#F8766D" "#EF7F49" "#E58700" "#D89000" "#C99800" "#B79F00" "#A3A500"
## [8] "#8AAB00" "#6BB100" "#39B600" "#00BA38" "#00BD5F" "#00BF7D" "#00C097"
## [15] "#00C0AF" "#00BFC4" "#00BCD8" "#00B7E9" "#00B0F6" "#00A7FF" "#619CFF"
## [22] "#9590FF" "#B983FF" "#D376FF" "#E76BF3" "#F564E3" "#FD61D1" "#FF62BC"
## [29] "#FF67A4" "#FE6E8A"
## [1] "colors used"
## [1] "#F8766D" "#F07F4B" "#E58709" "#D98F00" "#CB9700" "#BA9E00" "#A7A400"
## [8] "#90AA00" "#74B000" "#4CB400" "#00B825" "#00BC53" "#00BE72" "#00C08D"
## [15] "#00C1A5" "#00C0BA" "#00BECE" "#00BAE0" "#00B4EF" "#00ADFB" "#1EA3FF"
## [22] "#7498FF" "#A08CFF" "#C07FFF" "#D873FC" "#EA6AF0" "#F763E1" "#FE61CE"
## [29] "#FF62BA" "#FF67A3" "#FE6E89"
## [1] "colors used"
## [1] "#F8766D" "#F07E4C" "#E68613" "#DA8E00" "#CD9600" "#BD9D00" "#ABA300"
## [8] "#96A900" "#7CAE00" "#59B300" "#0CB702" "#00BB46" "#00BE67" "#00C082"
## [15] "#00C19A" "#00C0B0" "#00BFC4" "#00BCD7" "#00B8E7" "#00B1F4" "#00A9FF"
## [22] "#49A0FF" "#8494FF" "#AA88FF" "#C77CFF" "#DD71FA" "#ED68ED" "#F862DE"
## [29] "#FF61CC" "#FF63B8" "#FF68A1" "#FE6E88"
## [1] "colors used"
## [1] "#F8766D" "#F07E4D" "#E78619" "#DB8E00" "#CE9500" "#BF9C00" "#AEA200"
## [8] "#9AA800" "#82AD00" "#64B200" "#32B600" "#00BA38" "#00BD5C" "#00BF78"
## [15] "#00C091" "#00C1A7" "#00C0BB" "#00BECD" "#00BADE" "#00B5ED" "#00AEF9"
## [22] "#00A6FF" "#619CFF" "#9191FF" "#B385FF" "#CD79FF" "#E16FF8" "#EF67EB"
## [29] "#F962DB" "#FF61CA" "#FF63B6" "#FF68A0" "#FD6F88"
## [1] "colors used"
## [1] "#F8766D" "#F07E4E" "#E7851E" "#DD8D00" "#D09400" "#C29B00" "#B2A100"
## [8] "#9FA700" "#89AC00" "#6DB100" "#45B500" "#00B927" "#00BC51" "#00BE6E"
## [15] "#00C087" "#00C19D" "#00C0B2" "#00BFC4" "#00BCD6" "#00B8E5" "#00B3F2"
## [22] "#00ABFC" "#29A3FF" "#7398FF" "#9C8DFF" "#BA82FF" "#D277FF" "#E46DF5"
## [29] "#F166E8" "#FA62D9" "#FF61C7" "#FF63B4" "#FF689E" "#FD6F87"
## [1] "colors used"
## [1] "#F8766D" "#F17E4F" "#E88523" "#DE8C00" "#D29300" "#C49A00" "#B4A000"
## [8] "#A3A500" "#8EAB00" "#75AF00" "#53B400" "#00B70C" "#00BB45" "#00BD64"
## [15] "#00BF7D" "#00C094" "#00C1A8" "#00C0BB" "#00BECD" "#00BBDD" "#00B6EB"
## [22] "#00B0F6" "#00A8FF" "#4B9FFF" "#8195FF" "#A58AFF" "#C17FFF" "#D774FD"
## [29] "#E76BF3" "#F365E6" "#FB61D7" "#FF61C5" "#FF64B2" "#FF699D" "#FD6F86"
## [1] "colors used"
## [1] "#F8766D" "#F17D50" "#E88526" "#DE8C00" "#D39200" "#C69900" "#B79F00"
## [8] "#A6A400" "#93AA00" "#7CAE00" "#5EB300" "#2BB600" "#00BA38" "#00BC5A"
## [15] "#00BF74" "#00C08B" "#00C19F" "#00C0B3" "#00BFC4" "#00BDD5" "#00B9E3"
## [22] "#00B4F0" "#00ADFA" "#00A5FF" "#619CFF" "#8E92FF" "#AE87FF" "#C77CFF"
## [29] "#DB72FB" "#EA6AF1" "#F564E3" "#FC61D4" "#FF61C3" "#FF64B0" "#FF699C"
## [36] "#FD6F86"
## [1] "colors used"
## [1] "#F8766D" "#F17D51" "#E98429" "#DF8B00" "#D49200" "#C89800" "#BA9E00"
## [8] "#AAA300" "#97A800" "#82AD00" "#67B100" "#3FB500" "#00B929" "#00BC4F"
## [15] "#00BE6B" "#00BF82" "#00C097" "#00C1AA" "#00C0BC" "#00BECD" "#00BBDC"
## [22] "#00B7E9" "#00B1F4" "#00AAFE" "#30A2FF" "#7299FF" "#988FFF" "#B584FF"
## [29] "#CC7AFF" "#DE70F9" "#EC68EE" "#F663E1" "#FD61D2" "#FF61C1" "#FF64AF"
## [36] "#FF699B" "#FD6F85"
## [1] "colors used"
## [1] "#F8766D" "#F17D52" "#E9842C" "#E08B00" "#D69100" "#CA9700" "#BC9D00"
## [8] "#ADA200" "#9CA700" "#87AC00" "#6FB000" "#4DB400" "#00B813" "#00BB44"
## [15] "#00BD61" "#00BF79" "#00C08E" "#00C1A2" "#00C0B4" "#00BFC4" "#00BDD4"
## [22] "#00B9E2" "#00B5EE" "#00AFF8" "#00A7FF" "#4D9FFF" "#7F96FF" "#A18BFF"
## [29] "#BC81FF" "#D177FF" "#E26EF7" "#EE67EC" "#F863DF" "#FE61D0" "#FF62BF"
## [36] "#FF65AD" "#FF6A9A" "#FD7084"
## [1] "colors used"
## [1] "#F8766D" "#F27D52" "#EA842F" "#E18A00" "#D79000" "#CB9600" "#BE9C00"
## [8] "#B0A100" "#9FA600" "#8CAB00" "#75AF00" "#58B300" "#24B700" "#00BA38"
## [15] "#00BC58" "#00BE70" "#00C086" "#00C199" "#00C1AB" "#00C0BC" "#00BECC"
## [22] "#00BBDA" "#00B7E7" "#00B2F3" "#00ACFC" "#00A5FF" "#619CFF" "#8B93FF"
## [29] "#A989FF" "#C27FFF" "#D575FE" "#E56DF5" "#F066EA" "#F962DD" "#FE61CE"
## [36] "#FF62BD" "#FF65AC" "#FF6A99" "#FD7084"
## [1] "colors used"
## [1] "#F8766D" "#F27D53" "#EA8331" "#E28A00" "#D89000" "#CD9600" "#C09B00"
## [8] "#B2A000" "#A3A500" "#91AA00" "#7CAE00" "#61B200" "#39B600" "#00B92A"
## [15] "#00BB4E" "#00BE67" "#00BF7D" "#00C091" "#00C1A3" "#00C0B4" "#00BFC4"
## [22] "#00BDD3" "#00BAE0" "#00B5EC" "#00B0F6" "#00A9FF" "#35A2FF" "#7099FF"
## [29] "#9590FF" "#B186FF" "#C77CFF" "#D973FC" "#E76BF3" "#F265E8" "#FA62DB"
## [36] "#FF61CC" "#FF62BC" "#FF65AA" "#FF6A98" "#FD7083"
## [1] "colors used"
## [1] "#F8766D" "#F27D54" "#EB8333" "#E28900" "#D98F00" "#CE9500" "#C29A00"
## [8] "#B5A000" "#A6A400" "#95A900" "#81AD00" "#69B100" "#48B500" "#00B817"
## [15] "#00BB44" "#00BD5F" "#00BF75" "#00C089" "#00C19C" "#00C1AD" "#00C0BD"
## [22] "#00BECC" "#00BCD9" "#00B8E6" "#00B3F1" "#00AEFA" "#00A7FF" "#4F9FFF"
## [29] "#7D96FF" "#9E8DFF" "#B783FF" "#CC7AFF" "#DC71FA" "#EA6AF1" "#F365E6"
## [36] "#FB61D9" "#FF61CA" "#FF62BA" "#FF66A9" "#FF6B97" "#FD7083"
## [1] "colors used"
## [1] "#F8766D" "#F27C55" "#EB8335" "#E38900" "#DA8F00" "#CF9400" "#C49A00"
## [8] "#B79F00" "#A9A400" "#99A800" "#86AC00" "#70B000" "#53B400" "#1DB700"
## [15] "#00BA38" "#00BC56" "#00BE6D" "#00BF81" "#00C094" "#00C1A5" "#00C0B5"
## [22] "#00BFC4" "#00BDD2" "#00BADF" "#00B6EB" "#00B1F5" "#00ABFD" "#06A4FF"
## [29] "#619CFF" "#8893FF" "#A58AFF" "#BD81FF" "#D078FF" "#DF70F8" "#EC69EF"
## [36] "#F564E3" "#FB61D7" "#FF61C8" "#FF63B9" "#FF66A8" "#FF6B96" "#FC7082"
